[Wien] Space group change during running x sgroup
Peeyush Kumar Kamlesh
peeyush.physik.rku at gmail.com
Sat Jul 25 06:07:33 CEST 2020
Thank you so much Prof.Gavin. It is really very helpful.
Thank you again!
On Sat, Jul 25, 2020 at 6:25 AM Peeyush Kumar Kamlesh <
peeyush.physik.rku at gmail.com> wrote:
> Sir,
> One more question. How can I know the space group of the supercell? I
> searched but was unable to find it.
> Thank you!
>
> On Sat, Jul 25, 2020 at 6:20 AM Peeyush Kumar Kamlesh <
> peeyush.physik.rku at gmail.com> wrote:
>
>> Thank you So much Prof. Blaha. It is working now.
>>
>>
>>
>> On Fri, Jul 24, 2020 at 3:39 PM Peeyush Kumar Kamlesh <
>> peeyush.physik.rku at gmail.com> wrote:
>>
>>> Sir,
>>> Output of x nn is:
>>> -----------------------------------------
>>>
>>> specify nn-bondlength factor: (usually=2) [and optionally dlimit, dstmax (about
>>> 1.d-5, 20)]
>>> DSTMAX: 30.2976897600000
>>> iix,iiy,iiz 2 2 2 54.5904320000000
>>> 54.5904320000000 54.5904320000000
>>>
>>> ATOM 1 Rb ATOM 41 Zn
>>> RMT( 1)=2.50000 AND RMT( 41)=2.50000
>>> SUMS TO 5.00000 LT. NN-DIST= 5.89806
>>>
>>> And so on till
>>>
>>> ATOM 96 Bi ATOM 40 Zn
>>> RMT( 96)=2.50000 AND RMT( 40)=2.50000
>>> SUMS TO 5.00000 LT. NN-DIST= 5.90959
>>> WARNING: Mult not equal. PLEASE CHECK outputnn-file
>>> WARNING: Mult not equal. PLEASE CHECK outputnn-file
>>>
>>> --------------------------------------------
>>>
>>> When I ignore this warning and accept the changes produced by nn, then
>>> it pops up a new question (Use new struct-file?). on clicking on YES, it
>>> Displays a message:
>>>
>>>
>>> *Case-001.struct_nn copied to case-001.struct old struct-file saved as
>>> case-001.struct_init case-001.inst updated*
>>> And ask to start StructGen again.
>>> On ignoring this question, when I click on x sgroup, it shows following
>>> warning:
>>>
>>> *warning: !!! Number of inequivalent atoms has changed. !!! Old value=
>>> 34 New value= 40 warning: !!! Bravais lattice has changed. sgroup found: 35
>>> (C m m 2) Note that shift vectors for this space group are defined.*
>>> On further proceeding, it reflects an error in dstart;-
>>>
>>> *ROTDEF - Error
>>> 0.0u 0.0s 0:00.68 4.4% 0+0k 29488+24io 82pf+0w*
>>>
>>> On the contrary, if I agree on start StructGen again, and run x sgroup
>>> then it again show the following warning:
>>>
>>> *warning: !!! Number of inequivalent atoms has changed. !!! Old value=
>>> 96 New value= 40 warning: !!! Bravais lattice has changed. sgroup found: 35
>>> (C m m 2) Note that shift vectors for this space group are defined.*
>>> *warning: !!! Bravais lattice has changed.*
>>> And ask to accept a new file generated by sgroup. When I accept it then
>>> in further process, it does not show any error.
>>>
>>> But in the Phonopy manual it has been written that, *"Calculate forces
>>> on atoms in the supercells with displacements. It is necessary to use
>>> case.struct_nn file when running init_lapw. Note that case.struct_sgroup
>>> file can’t be used with phonopy."*
>>>
>>> *I am confused, how should I proceed further?*
>>>
>>> Thank you!
>>>
>>>
>>> On Fri, Jul 24, 2020 at 11:56 AM Peeyush Kumar Kamlesh <
>>> peeyush.physik.rku at gmail.com> wrote:
>>>
>>>> Dear Blaha Sir,
>>>> 1. First I prepared a case.struct file with optimized lattice
>>>> parameters, having F43m spacegroup (216). Which F lattice. it is as follows:
>>>> ----------------------------------------------------------
>>>>
>>>> F LATTICE,NONEQUIV.ATOMS: 3 216_F-43m
>>>> MODE OF CALC=RELA unit=ang
>>>> 13.647608 13.647608 13.647608 90.000000 90.000000 90.000000
>>>> ATOM 1: X=0.50000000 Y=0.50000000 Z=0.50000000
>>>> MULT= 1 ISPLIT= 2
>>>> Rb NPT= 781 R0=0.00001000 RMT= 2.5000 Z: 37.000
>>>> LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
>>>> 0.0000000 1.0000000 0.0000000
>>>> 0.0000000 0.0000000 1.0000000
>>>> ATOM 2: X=0.25000000 Y=0.25000000 Z=0.25000000
>>>> MULT= 1 ISPLIT= 2
>>>> Zn NPT= 781 R0=0.00005000 RMT= 2.5000 Z: 30.000
>>>> LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
>>>> 0.0000000 1.0000000 0.0000000
>>>> 0.0000000 0.0000000 1.0000000
>>>> ATOM 3: X=0.00000000 Y=0.00000000 Z=0.00000000
>>>> MULT= 1 ISPLIT= 2
>>>> Bi NPT= 781 R0=0.00000500 RMT= 2.5000 Z: 83.000
>>>> LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
>>>> 0.0000000 1.0000000 0.0000000
>>>> 0.0000000 0.0000000 1.0000000
>>>> 24 NUMBER OF SYMMETRY OPERATIONS
>>>>
>>>> ------------------------------------------------------------------------------------
>>>> 2. Then I created a supercell (1x1x1) using wien2k, having P lattice
>>>> but with the same space group. case_super .struct file is as follows:
>>>> -----------------------------------------------------------
>>>>
>>>> P LATTICE,NONEQUIV. ATOMS 12
>>>> MODE OF CALC=RELA unit=ang
>>>> 13.647608 13.647608 13.647608 90.000000 90.000000 90.000000
>>>> ATOM 1: X=0.50000000 Y=0.50000000 Z=0.50000000
>>>> MULT= 1 ISPLIT= 2
>>>> Rb NPT= 781 R0=0.00001000 RMT= 2.5000 Z: 37.0
>>>> LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
>>>> 0.0000000 1.0000000 0.0000000
>>>> 0.0000000 0.0000000 1.0000000
>>>> And so on ................. till
>>>> ATOM 12: X=0.00000000 Y=0.50000000 Z=0.50000000
>>>> MULT= 1 ISPLIT= 2
>>>> Bi NPT= 781 R0=0.00000500 RMT= 2.5000 Z: 83.0
>>>> LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
>>>> 0.0000000 1.0000000 0.0000000
>>>> 0.0000000 0.0000000 1.0000000
>>>> 0 NUMBER OF SYMMETRY OPERATIONS
>>>> -------------------------------------------------------------
>>>> 3. Then I copied case_super.struct to case.struct file and used the
>>>> command (phonopy --wien2k -d --dim="2 2 2" -c case.struct) to run phonopy
>>>> with a supercell of (2x2x2). its output is as follows:
>>>> ---------------------------------------------------
>>>> _
>>>> _ __ | |__ ___ _ __ ___ _ __ _ _
>>>> | '_ \| '_ \ / _ \| '_ \ / _ \ | '_ \| | | |
>>>> | |_) | | | | (_) | | | | (_) || |_) | |_| |
>>>> | .__/|_| |_|\___/|_| |_|\___(_) .__/ \__, |
>>>> |_| |_| |___/
>>>> 2.7.0
>>>>
>>>> Python version 3.8.4
>>>> Spglib version 1.15.1
>>>>
>>>> Calculator interface: wien2k
>>>> Crystal structure was read from "RbZnBi.struct".
>>>> Unit of length: au
>>>> Displacements creation mode
>>>> Settings:
>>>> Supercell: [2 2 2]
>>>> Spacegroup: F-43m (216)
>>>> Use -v option to watch primitive cell, unit cell, and supercell
>>>> structures.
>>>>
>>>> Number of non-equivalent atoms in RbZnBi.structS-001.in: 40
>>>> Number of non-equivalent atoms in RbZnBi.structS-002.in: 38
>>>> Number of non-equivalent atoms in RbZnBi.structS-003.in: 40
>>>> "phonopy_disp.yaml" and supercells have been created.
>>>>
>>>> Summary of calculation was written in "phonopy_disp.yaml".
>>>> _
>>>> ___ _ __ __| |
>>>> / _ \ '_ \ / _` |
>>>> | __/ | | | (_| |
>>>> \___|_| |_|\__,_|
>>>> ------------------------------------------------------------------------
>>>>
>>>> 4. It is clear from the output that the space group is not changed. It
>>>> generates one file for a perfect supercell and 3 files (case-xxx.struct)
>>>> for supercells with displacements. case-xxx.struct is as follows:
>>>> ---------------------------------------------------
>>>> Title
>>>> P LATTICE,NONEQUIV.ATOMS: 96
>>>> MODE OF CALC=RELA
>>>> 27.295216 27.295216 27.295216 90.000000 90.000000 90.000000
>>>> ATOM -1: X=0.25073273 Y=0.25000000 Z=0.25000000
>>>> MULT= 1 ISPLIT= 8
>>>> Rb NPT= 781 R0=0.00001000 RMT= 2.50000 Z: 37.0
>>>> LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
>>>> 0.0000000 1.0000000 0.0000000
>>>> 0.0000000 0.0000000 1.0000000
>>>> And so on.........till
>>>> ATOM -96: X=0.50000000 Y=0.75000000 Z=0.75000000
>>>> MULT= 1 ISPLIT= 8
>>>> Bi NPT= 781 R0=0.00000500 RMT= 3.0000 Z: 83.000
>>>> LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
>>>> 0.0000000 1.0000000 0.0000000
>>>> 0.0000000 0.0000000 1.0000000
>>>> 0 NUMBER OF SYMMETRY OPERATIONS
>>>>
>>>> --------------------------------------------------------------------------------------
>>>> 5. Then I picked one of the case-xxx.struct files and put in another
>>>> directory for initialization and started step by step initialization. and
>>>> perform x nn: Which Shows following warning:
>>>>
>>>> WARNING: Mult not equal. PLEASE CHECK outputnn-file
>>>> WARNING: ityp not equal. PLEASE CHECK outputnn-file
>>>>
>>>> 6. Then I tried to increase RMT up 3. It now shows the following message:
>>>> ERROR !!!!!!!!!!!!!!!
>>>> RMT( 1)=3.00000 AND RMT( 41)=3.00000
>>>> SUMS TO 6.00000 GT NNN-DIST= 5.89806
>>>> WARNING: Mult not equal. PLEASE CHECK outputnn-file
>>>> WARNING: ityp not equal. PLEASE CHECK outputnn-file
>>>>
>>>> Please suggest What should I do? I shall be grateful to you!
>>>>
>>>> Thanks and Regards
>>>>
>>>>
>>>> On Fri, Jul 24, 2020 at 1:53 AM Peeyush Kumar Kamlesh <
>>>> peeyush.physik.rku at gmail.com> wrote:
>>>>
>>>>> Before that when I run the command x nn, it shows following error:
>>>>>
>>>>> WARNING: Mult not equal. PLEASE CHECK outputnn-file
>>>>> WARNING: ityp not equal. PLEASE CHECK outputnn-file
>>>>>
>>>>> I have tried by putting different values for nn, but it is not changing.
>>>>>
>>>>> What will be its solution?
>>>>>
>>>>>
>>>>> On Fri, Jul 24, 2020 at 1:33 AM Peeyush Kumar Kamlesh <
>>>>> peeyush.physik.rku at gmail.com> wrote:
>>>>>
>>>>>> Dear Wien2k users,
>>>>>> Greetings!
>>>>>> I am working on XYZ half-Heusler compounds with space group no.-216.
>>>>>> When I do initialization of a struct file of a supercell. then output of x
>>>>>> sgroup shows some warning:
>>>>>>
>>>>>> warning: !!! Number of inequivalent atoms has changed. !!! Old value=
>>>>>> 34 New value= 40 warning: !!! Bravais lattice has changed.
>>>>>> sgroup found: 35 (C m m 2) Note that shift vectors for this space
>>>>>> group are defined.
>>>>>> Bravais lattice: Orthorhombic C-base centred.
>>>>>> Kindly help me to solve the problem.
>>>>>>
>>>>>> Thank you!
>>>>>>
>>>>>
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